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- PDB-7cl6: The crystal structure of KanJ in complex with neamine and N-oxaly... -

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Basic information

Entry
Database: PDB / ID: 7cl6
TitleThe crystal structure of KanJ in complex with neamine and N-oxalylglycine
ComponentsKanamycin B dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / kanamycin biosynthesis
Function / homologykanamycin B dioxygenase / kanamycin biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / NICKEL (II) ION / N-OXALYLGLYCINE / Chem-XXX / Kanamycin B dioxygenase
Function and homology information
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsKitayama, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: Chembiochem / Year: 2021
Title: Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Authors: Kudo, F. / Kitayama, Y. / Miyanaga, A. / Numakura, M. / Eguchi, T.
History
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kanamycin B dioxygenase
B: Kanamycin B dioxygenase
C: Kanamycin B dioxygenase
D: Kanamycin B dioxygenase
E: Kanamycin B dioxygenase
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,79424
Polymers201,6256
Non-polymers3,16918
Water4,540252
1
A: Kanamycin B dioxygenase
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2658
Polymers67,2082
Non-polymers1,0566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Kanamycin B dioxygenase
hetero molecules

D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2658
Polymers67,2082
Non-polymers1,0566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
3
E: Kanamycin B dioxygenase
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2658
Polymers67,2082
Non-polymers1,0566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.340, 185.227, 109.493
Angle α, β, γ (deg.)90.000, 94.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA2 - 28118 - 297
21ALAALAPROPROBB2 - 28118 - 297
12HISHISVALVALAA0 - 28416 - 300
22HISHISVALVALCC0 - 28416 - 300
13HISHISHISHISAA0 - 27516 - 291
23HISHISHISHISDD0 - 27516 - 291
14HISHISVALVALAA0 - 28416 - 300
24HISHISVALVALEE0 - 28416 - 300
15HISHISVALVALAA0 - 27316 - 289
25HISHISALAALAFF0 - 28316 - 299
16ALAALAGLYGLYBB2 - 27818 - 294
26ALAALAALAALACC2 - 28318 - 299
17ALAALAHISHISBB2 - 27518 - 291
27ALAALAHISHISDD2 - 27518 - 291
18ALAALAPROPROBB2 - 28118 - 297
28ALAALAPROPROEE2 - 28118 - 297
19ALAALAVALVALBB2 - 27318 - 289
29ALAALAALAALAFF2 - 28318 - 299
110HISHISHISHISCC0 - 28016 - 296
210HISHISHISHISDD0 - 27516 - 291
111HISHISVALVALCC0 - 28416 - 300
211HISHISVALVALEE0 - 28416 - 300
112HISHISVALVALCC0 - 28416 - 300
212HISHISVALVALFF0 - 28416 - 300
113HISHISHISHISDD0 - 27516 - 291
213HISHISHISHISEE0 - 27516 - 291
114HISHISVALVALDD0 - 27316 - 289
214HISHISALAALAFF0 - 28316 - 299
115HISHISVALVALEE0 - 27316 - 289
215HISHISALAALAFF0 - 28316 - 299

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Kanamycin B dioxygenase / Kanamycin biosynthesis protein J


Mass: 33604.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: kanJ, kacB / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / References: UniProt: Q6L732, kanamycin B dioxygenase
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Sugar
ChemComp-XXX / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside / Neamine


Type: D-saccharide / Mass: 322.358 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26N4O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Lithium sulfate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 73990 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.053 / Rrim(I) all: 0.078 / Net I/σ(I): 13.3
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4591 / CC1/2: 0.674 / Rpim(I) all: 0.496 / Rrim(I) all: 0.732 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CL2

7cl2


Resolution: 2.44→47.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.034 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3546 4.8 %RANDOM
Rwork0.1897 ---
obs0.1912 70405 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.92 Å2 / Biso mean: 51.065 Å2 / Biso min: 22.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20.65 Å2
2---0.06 Å20 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 2.44→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13107 0 198 252 13557
Biso mean--50.63 41.15 -
Num. residues----1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313709
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712489
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.64818859
X-RAY DIFFRACTIONr_angle_other_deg1.2231.5729016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52751668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89221.32727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.249151960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.11415102
X-RAY DIFFRACTIONr_chiral_restr0.0680.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022706
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87850.05
12B87850.05
21A89060.05
22C89060.05
31A88530.04
32D88530.04
41A89380.05
42E89380.05
51A86620.05
52F86620.05
61B86570.06
62C86570.06
71B87050.05
72D87050.05
81B87710.05
82E87710.05
91B85390.05
92F85390.05
101C87660.05
102D87660.05
111C88350.06
112E88350.06
121C87410.05
122F87410.05
131D87290.05
132E87290.05
141D86610.06
142F86610.06
151E86260.05
152F86260.05
LS refinement shellResolution: 2.44→2.503 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 248 -
Rwork0.293 5222 -
all-5470 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1267-0.12180.31050.9859-0.11421.0270.10920.0319-0.1261-0.08160.08410.00740.11150.0436-0.19340.27970.0065-0.05310.1105-0.03660.0596-13.33950.06192.507
20.8997-0.3225-0.16071.54470.21990.65170.1149-0.005-0.0352-0.205-0.0186-0.1327-0.115-0.0132-0.09640.3409-0.01560.01910.14020.00780.0286-28.45883.70178.442
30.9658-0.22040.58930.6213-0.03322.2779-0.110.08570.05550.1293-0.0583-0.0880.09690.01570.16840.31830.0281-0.03330.17810.00120.0269-12.8058.168-4.775
40.9576-0.0053-0.22181.0184-0.26462.0330.0836-0.02550.119-0.1626-0.0909-0.00840.0625-0.19390.00720.32560.0327-0.00380.1726-0.00710.016323.32313.415-41.44
51.00920.67020.71571.24170.64572.01590.22570.1923-0.1670.44630.1413-0.27290.35940.3308-0.36690.46280.1641-0.25190.199-0.14330.166111.01834.1120.573
60.57570.238-0.61031.90732.50445.36910.0756-0.0216-0.004-0.5099-0.06630.1106-0.92020.0224-0.00930.43970.0884-0.12890.1393-0.10550.1285.24267.07441.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 303
2X-RAY DIFFRACTION2B2 - 303
3X-RAY DIFFRACTION3C0 - 303
4X-RAY DIFFRACTION4D0 - 303
5X-RAY DIFFRACTION5E0 - 303
6X-RAY DIFFRACTION6F0 - 303

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